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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings OmnipathR_3.10.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.10.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'OmnipathR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... NOTE
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:44] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-06 04:44:57] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
collectri                            77.25   1.48   78.96
annotation_categories                61.72   0.08   62.40
dorothea                             44.13   0.66   45.61
curated_ligrec_stats                 23.55   1.66   66.55
filter_extra_attrs                   14.83   0.11   15.33
pivot_annotations                    11.58   0.60   13.84
nichenet_gr_network_omnipath         10.54   0.48   11.39
extra_attr_values                     9.64   0.23   10.22
with_extra_attrs                      9.19   0.19    9.87
giant_component                       8.92   0.17    9.56
extra_attrs_to_cols                   8.73   0.12    8.88
go_annot_download                     8.06   0.53    7.63
static_table                          7.60   0.27    8.09
nichenet_signaling_network_omnipath   7.53   0.19    8.28
print_interactions                    6.08   0.23    7.80
filter_intercell                      5.62   0.33    5.97
extra_attrs                           5.30   0.02    5.31
omnipath                              5.09   0.00    5.10
pubmed_open                           4.87   0.22    5.58
filter_by_resource                    4.69   0.11    5.43
curated_ligand_receptor_interactions  3.85   0.50    9.98
annotated_network                     1.53   0.12    5.40
ensembl_id_mapping_table              0.75   0.08   32.05
with_references                       0.61   0.06    6.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.